Atomistry » Sodium » PDB 6ahh-6awy » 6amh
Atomistry »
  Sodium »
    PDB 6ahh-6awy »
      6amh »

Sodium in PDB 6amh: Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB4D11 with Ser Bound As E(AEX1)

Enzymatic activity of Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB4D11 with Ser Bound As E(AEX1)

All present enzymatic activity of Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB4D11 with Ser Bound As E(AEX1):
4.2.1.20;

Protein crystallography data

The structure of Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB4D11 with Ser Bound As E(AEX1), PDB code: 6amh was solved by A.R.Buller, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 1.63
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.756, 109.600, 160.882, 90.00, 90.00, 90.00
R / Rfree (%) 20.7 / 23.3

Sodium Binding Sites:

The binding sites of Sodium atom in the Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB4D11 with Ser Bound As E(AEX1) (pdb code 6amh). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB4D11 with Ser Bound As E(AEX1), PDB code: 6amh:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 6amh

Go back to Sodium Binding Sites List in 6amh
Sodium binding site 1 out of 4 in the Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB4D11 with Ser Bound As E(AEX1)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB4D11 with Ser Bound As E(AEX1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:36.2
occ:1.00
 O A:HOH506 2.4 32.9 1.0
O A:HOH602 2.5 32.2 1.0
O A:TYR301 2.7 28.4 1.0
O A:GLY303 2.7 25.7 1.0
O A:SER263 2.9 28.1 1.0
OG A:SER263 3.2 29.0 1.0
OG A:SER265 3.3 28.7 1.0
O A:GLY227 3.6 21.7 1.0
C A:GLY303 3.8 26.7 1.0
O A:HOH574 3.9 20.6 1.0
C A:TYR301 3.9 28.9 1.0
C A:SER263 3.9 28.5 1.0
CB A:SER265 4.0 28.7 1.0
N A:GLY303 4.1 28.6 1.0
N A:SER265 4.3 29.0 1.0
CB A:SER263 4.3 29.1 1.0
C A:PRO302 4.3 29.8 1.0
C A:GLY227 4.3 21.0 1.0
CA A:GLY303 4.4 28.1 1.0
CA A:PRO302 4.6 30.1 1.0
CA A:SER263 4.6 29.0 1.0
N A:PRO302 4.7 29.9 1.0
CA A:GLY227 4.7 20.6 1.0
O A:PRO302 4.8 30.6 1.0
CA A:SER265 4.8 29.4 1.0
OE2 A:GLU251 4.8 24.8 1.0
N A:VAL304 4.8 26.2 1.0
O A:VAL226 4.9 21.1 1.0
CA A:TYR301 4.9 28.7 1.0
N A:ALA264 5.0 28.9 1.0

Sodium binding site 2 out of 4 in 6amh

Go back to Sodium Binding Sites List in 6amh
Sodium binding site 2 out of 4 in the Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB4D11 with Ser Bound As E(AEX1)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB4D11 with Ser Bound As E(AEX1) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na402

b:33.0
occ:1.00
 O B:TYR301 2.6 35.6 1.0
O B:HOH577 2.7 35.9 1.0
O B:GLY303 2.8 34.4 1.0
O B:SER263 2.9 39.7 1.0
OG B:SER265 3.0 40.2 1.0
OG B:SER263 3.1 39.7 1.0
O B:GLY227 3.7 29.4 1.0
CB B:SER265 3.8 40.2 1.0
C B:GLY303 3.8 35.2 1.0
C B:TYR301 3.9 36.0 1.0
C B:SER263 3.9 40.4 1.0
O B:HOH559 4.0 27.5 1.0
CB B:SER263 4.1 40.2 1.0
C B:PRO302 4.2 38.1 1.0
N B:GLY303 4.2 37.2 1.0
N B:SER265 4.3 40.8 1.0
C B:GLY227 4.4 28.8 1.0
O B:PRO302 4.4 38.9 1.0
CA B:GLY303 4.5 36.8 1.0
CA B:SER263 4.5 40.5 1.0
CA B:PRO302 4.6 38.2 1.0
CA B:SER265 4.7 41.0 1.0
N B:PRO302 4.7 37.3 1.0
CA B:GLY227 4.7 28.2 1.0
CA B:TYR301 4.8 35.0 1.0
OG B:SER292 4.8 61.6 1.0
OE2 B:GLU251 4.9 34.2 1.0
N B:VAL304 4.9 34.7 1.0
N B:TYR301 4.9 34.2 1.0
O B:VAL226 5.0 27.9 1.0
CB B:VAL304 5.0 33.5 1.0
CB B:TYR301 5.0 34.5 1.0

Sodium binding site 3 out of 4 in 6amh

Go back to Sodium Binding Sites List in 6amh
Sodium binding site 3 out of 4 in the Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB4D11 with Ser Bound As E(AEX1)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB4D11 with Ser Bound As E(AEX1) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na402

b:31.9
occ:1.00
 O C:HOH515 2.6 25.9 1.0
O C:TYR301 2.6 26.2 1.0
O C:HOH558 2.8 25.9 1.0
O C:GLY303 2.8 24.8 1.0
O C:SER263 2.8 27.4 1.0
OG C:SER263 3.1 28.6 1.0
OG C:SER265 3.1 28.1 1.0
C C:SER263 3.8 27.3 1.0
CB C:SER265 3.8 28.3 1.0
C C:TYR301 3.8 26.5 1.0
C C:GLY303 3.9 25.6 1.0
O C:GLY227 3.9 22.2 1.0
O C:HOH575 3.9 19.5 1.0
CB C:SER263 4.1 28.3 1.0
N C:GLY303 4.1 27.1 1.0
C C:PRO302 4.2 27.8 1.0
N C:SER265 4.2 28.1 1.0
CA C:SER263 4.4 27.6 1.0
CA C:PRO302 4.4 27.9 1.0
CA C:GLY303 4.4 26.8 1.0
C C:GLY227 4.5 21.9 1.0
O C:PRO302 4.6 28.7 1.0
N C:PRO302 4.6 27.5 1.0
CA C:SER265 4.7 28.4 1.0
OE2 C:GLU251 4.7 24.7 1.0
CA C:TYR301 4.9 26.1 1.0
N C:ALA264 4.9 27.3 1.0
N C:VAL304 4.9 25.5 1.0
CA C:GLY227 4.9 21.4 1.0

Sodium binding site 4 out of 4 in 6amh

Go back to Sodium Binding Sites List in 6amh
Sodium binding site 4 out of 4 in the Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB4D11 with Ser Bound As E(AEX1)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Engineered Tryptophan Synthase B-Subunit From Pyrococcus Furiosus, PFTRPB4D11 with Ser Bound As E(AEX1) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na402

b:29.9
occ:1.00
 O D:HOH560 2.4 35.7 1.0
O D:HOH594 2.5 29.8 1.0
O D:TYR301 2.6 30.5 1.0
O D:SER263 2.8 29.7 1.0
O D:GLY303 2.8 28.9 1.0
OG D:SER265 2.9 33.8 1.0
OG D:SER263 3.1 30.0 1.0
O D:GLY227 3.8 25.3 1.0
CB D:SER265 3.8 33.7 1.0
O D:HOH516 3.8 24.4 1.0
C D:TYR301 3.8 30.8 1.0
C D:SER263 3.9 30.4 1.0
C D:GLY303 3.9 29.6 1.0
CB D:SER263 4.0 29.9 1.0
C D:PRO302 4.2 31.5 1.0
N D:SER265 4.2 32.6 1.0
N D:GLY303 4.3 30.9 1.0
C D:GLY227 4.3 25.0 1.0
CA D:SER263 4.4 30.6 1.0
O D:PRO302 4.5 31.8 1.0
CA D:GLY303 4.5 30.6 1.0
CA D:PRO302 4.5 31.8 1.0
CA D:SER265 4.7 33.9 1.0
CA D:GLY227 4.7 24.5 1.0
N D:PRO302 4.7 31.6 1.0
CA D:TYR301 4.8 30.6 1.0
OE2 D:GLU251 4.8 26.8 1.0
OG D:SER292 4.9 33.6 1.0
N D:VAL304 4.9 29.5 1.0
CB D:TYR301 4.9 30.6 1.0
N D:TYR301 4.9 29.8 1.0
O D:VAL226 4.9 24.1 1.0
N D:ALA264 5.0 31.1 1.0

Reference:

A.R.Buller, P.Van Roye, J.K.B.Cahn, R.A.Scheele, M.Herger, F.H.Arnold. Directed Evolution Mimics Allosteric Activation By Stepwise Tuning of the Conformational Ensemble. J. Am. Chem. Soc. V. 140 7256 2018.
ISSN: ESSN 1520-5126
PubMed: 29712420
DOI: 10.1021/JACS.8B03490
Page generated: Tue Oct 8 01:51:18 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy